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LRRC8A-dcpib in MSP1E3D1 nanodisc expanded state

Analyse LRRC8A-dcpib in MSP1E3D1 nanodisc expanded state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6NZZ
Type: protein
Length: 1,836 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Volume-regulated anion channel subunit LRRC8A
UniProt: Q80WG5
Ligands: POV, L9Y
Pockets: 20 · best druggability 0.82

Structure

electron microscopy · 1 distinct chain · 62% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Volume-regulated anion channel subunit LRRC8A	protein	306	62% helix, 5% strand	Q80WG5

Ligands and binding sites

POV · (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate · ligand · 18 copies · chains A, B, F, C, D, E
L9Y · 4-{[(2S)-2-butyl-6,7-dichloro-2-cyclopentyl-1-oxo-2,3-dihydro-1H-inden-5-yl]oxy}butanoic acid · ligand · chains A, B, C, D, E, F

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	922	0.82	0.84	93	L9Y
2	782	0.82	0.85	81	empty
3	520	0.64	0.75	40	POV
4	507	0.64	0.76	42	POV
5	495	0.64	0.75	37	POV

Interfaces

6 interfaces between chains.

A–F · 1643 Å² buried · 15 hydrogen bonds · protein-protein
B–C · 1634 Å² buried · 13 hydrogen bonds · protein-protein
D–E · 1625 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 1569 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 1567 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 18 disulfide (disulfide).

Compared structures

6NZZ · LRRC8A-DCPIB in MSP1E3D1 nanodisc expanded state · the same entry in another collection · chain C against C, TM-score 1.00
Q80WG5 · AlphaFold monomer V2.0 prediction for volume-regulated anion channel subunit LRRC8A… · a predicted model of the same protein · chain A against A, TM-score 0.95

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q80WG5
Elsewhere: RCSB PDB 6NZZ · PDBe 6NZZ · UniProt Q80WG5

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